From where is the transaction fee for a custom token (build on Stellar) that is charged by Stellar Network? Is it from the custom wallet (I know the only possibility will be in XLM)? From whose Account are these XLMs deducted?
The transaction fee is deducted from the account that acts as the source account for the transaction envelope.
const account = await server.loadAccount(source);
const builder = new stellar.TransactionBuilder(account)